Dynamic usage of alternative splicing exons during mouse retina development
| Autor: | Tomohiro Masuda, Donald J. Zack, Jiang Qian, Jun Wan, Laszlo Hackler, Shannath L. Merbs, Kieron Torres |
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| Rok vydání: | 2011 |
| Předmět: |
Genetics
0303 health sciences Gene Expression Profiling Alternative splicing Exonic splicing enhancer Interrupted gene Intron Gene Expression Regulation Developmental Retina homeostasis Exons Gene Regulation Chromatin and Epigenetics Regulatory Sequences Ribonucleic Acid Biology Retina Alternative Splicing Mice 03 medical and health sciences Splicing factor Exon 0302 clinical medicine RNA splicing Animals 030217 neurology & neurosurgery 030304 developmental biology |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| DOI: | 10.1093/nar/gkr545 |
| Popis: | Alternative processing of pre-mRNA plays an important role in protein diversity and biological function. Previous studies on alternative splicing (AS) often focused on the spatial patterns of protein isoforms across different tissues. Here we studied dynamic usage of AS across time, during murine retina development. Over 7000 exons showed dynamical changes in splicing, with differential splicing events occurring more frequently in early development. The overall splicing patterns for exclusive and inclusive exons show symmetric trends and genes with symmetric splicing patterns that tend to have similar biological functions. Furthermore, we observed that within the retina, retina-enriched genes that are preferentially expressed at the adult stage tend to have more dynamically spliced exons compared to other genes, suggesting that genes maintaining retina homeostasis also play an important role in development via a series of AS events. Interestingly, the transcriptomes of retina-enriched genes largely reflect the retinal developmental process. Finally, we identified a number of candidate cis-regulatory elements for retinal AS by analyzing the relative occurrence of sequence motifs in exons or flanking introns. The occurrence of predicted regulatory elements showed strong correlation with the expression level of known RNA binding proteins, suggesting the high quality of the identified cis-regulatory elements. |
| Databáze: | OpenAIRE |
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